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        Note that additional data was saved in multiqc_data when this report was generated.

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        If you use plots from MultiQC in a publication or presentation, please cite:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411
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        Tool Citations

        Please remember to cite the tools that you use in your analysis.

        To help with this, you can download publication details of the tools mentioned in this report:

        About MultiQC

        This report was generated using MultiQC, version 1.30

        You can see a YouTube video describing how to use MultiQC reports here: https://youtu.be/qPbIlO_KWN0

        For more information about MultiQC, including other videos and extensive documentation, please visit http://multiqc.info

        You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: https://github.com/MultiQC/MultiQC

        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        This report has been generated by the nf-core/rnavar analysis pipeline. For information about how to interpret these results, please see the documentation.
        Report generated on 2025-10-02, 16:41 CEST based on data in: /work/user/fmt116/TP_nextflow/projet_nextflow/sra_tools/work/ba/4a8f4227590dc4822d79aeb5e47ff1

        General Statistics

        Showing 2/2 rows and 3/7 columns.
        Sample NameTotal readsAlignedAlignedUniq alignedUniq alignedMultimappedDuplication
        SRR2045415
        22.4M
        20.1M
        89.6%
        19.1M
        85.3%
        1.0M
        21.8%
        SRR2045416
        36.5M
        28.2M
        77.4%
        27.4M
        75.1%
        0.8M
        11.2%

        Read Alignment (STAR)

        Universal RNA-seq aligner.URL: https://github.com/alexdobin/STARDOI: 10.1093/bioinformatics/bts635

        Summary Statistics

        Summary statistics from the STAR alignment

        Showing 2/2 rows and 10/19 columns.
        Sample NameTotal readsAlignedAlignedUniq alignedUniq alignedMultimappedAvg. read lenAvg. mapped lenSplicesAnnotated splicesGT/AG splicesGC/AG splicesAT/AC splicesNon-canonical splicesMismatch rateDel rateDel lenIns rateIns len
        SRR2045415
        22.4M
        20.1M
        89.6%
        19.1M
        85.3%
        1.0M
        200.0bp
        197.3bp
        16.6M
        16.5M
        16.3M
        0.2M
        0.0M
        0.1M
        0.9%
        0.0%
        2.3bp
        0.0%
        1.9bp
        SRR2045416
        36.5M
        28.2M
        77.4%
        27.4M
        75.1%
        0.8M
        200.0bp
        196.9bp
        15.4M
        15.4M
        15.2M
        0.1M
        0.0M
        0.1M
        1.0%
        0.0%
        2.4bp
        0.0%
        1.9bp

        Alignment Scores

        Created with MultiQC

        Samtools Flagstat

        Toolkit for interacting with BAM/CRAM files.URL: http://www.htslib.orgDOI: 10.1093/bioinformatics/btp352

        Mapped reads per contig

        The samtools idxstats tool counts the number of mapped reads per chromosome / contig. Chromosomes with < 0.1% of the total aligned reads are omitted from this plot.

        Created with MultiQC

        GATK4 MarkDuplicates

        Metrics generated either by GATK4 MarkDuplicates.URL: http://broadinstitute.github.io/picard

        Mark Duplicates

        Number of reads, categorised by duplication state. Pair counts are doubled - see help text for details.

        The table in the Picard metrics file contains some columns referring read pairs and some referring to single reads.

        To make the numbers in this plot sum correctly, values referring to pairs are doubled according to the scheme below:

        • READS_IN_DUPLICATE_PAIRS = 2 * READ_PAIR_DUPLICATES
        • READS_IN_UNIQUE_PAIRS = 2 * (READ_PAIRS_EXAMINED - READ_PAIR_DUPLICATES)
        • READS_IN_UNIQUE_UNPAIRED = UNPAIRED_READS_EXAMINED - UNPAIRED_READ_DUPLICATES
        • READS_IN_DUPLICATE_PAIRS_OPTICAL = 2 * READ_PAIR_OPTICAL_DUPLICATES
        • READS_IN_DUPLICATE_PAIRS_NONOPTICAL = READS_IN_DUPLICATE_PAIRS - READS_IN_DUPLICATE_PAIRS_OPTICAL
        • READS_IN_DUPLICATE_UNPAIRED = UNPAIRED_READ_DUPLICATES
        • READS_UNMAPPED = UNMAPPED_READS
        Created with MultiQC

        Software Versions

        Software Versions lists versions of software tools extracted from file contents.

        GroupSoftwareVersion
        CAT_FASTQcat9.5
        FASTQCfastqc0.12.1
        GATK4_BEDTOINTERVALLISTgatk44.6.1.0
        GATK4_CREATESEQUENCEDICTIONARYgatk44.6.1.0
        GATK4_HAPLOTYPECALLERgatk44.6.1.0
        GATK4_INTERVALLISTTOOLSgatk44.6.1.0
        GATK4_MERGEVCFSgatk44.6.1.0
        GATK4_SPLITNCIGARREADSgatk44.6.1.0
        GATK4_VARIANTFILTRATIONgatk44.6.1.0
        GTF2BEDRscript3.5.1 (2018-07-02)
        PICARD_MARKDUPLICATESpicard3.3.0
        REMOVE_UNKNOWN_REGIONSpython3.8.3
        SAMTOOLS_FAIDXsamtools1.21
        SAMTOOLS_IDXSTATSsamtools1.21
        SAMTOOLS_INDEXsamtools1.21
        SAMTOOLS_MERGEsamtools1.21
        SAMTOOLS_SORTsamtools1.21
        SAMTOOLS_STATSsamtools1.21
        STAR_ALIGNgawk5.1.0
        samtools1.21
        star2.7.11b
        STAR_INDEXVERSIONgawk5.1.0
        samtools1.21
        star2.7.11b
        Samtools Flagstatsamtools1.21
        TABIXtabix1.21
        WorkflowNextflow25.04.0
        nf-core/rnavarv1.2.1-g2cbf046

        nf-core/rnavar Methods Description

        Suggested text and references to use when describing pipeline usage within the methods section of a publication.URL: https://github.com/nf-core/rnavar

        Methods

        Data was processed using nf-core/rnavar v1.2.1 (doi: 10.5281/zenodo.6669636) of the nf-core collection of workflows (Ewels et al., 2020), utilising reproducible software environments from the Bioconda (Grüning et al., 2018) and Biocontainers (da Veiga Leprevost et al., 2017) projects.

        The pipeline was executed with Nextflow v25.04.0 (Di Tommaso et al., 2017) with the following command:

        nextflow run nf-core/rnavar -r 1.2.1 -profile singularity --input /work/user/fmt116/TP_nextflow/projet_nextflow/sra_tools/input.csv --fasta /work/user/fmt116/TP_nextflow/projet_nextflow/sra_tools/GCF_902167405.1_gadMor3.0_genomic.fna --gtf /work/user/fmt116/TP_nextflow/projet_nextflow/sra_tools/genomic.gtf --aligner star --star_index /work/user/fmt116/TP_nextflow/projet_nextflow/sra_tools/star_index/ --fastqc_threads 4 --star_threads 12 --read_length 150 --outdir /work/user/fmt116/TP_nextflow/projet_nextflow/sra_tools/results_rnavar --skip_baserecalibration -resume

        References

        • Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., & Notredame, C. (2017). Nextflow enables reproducible computational workflows. Nature Biotechnology, 35(4), 316-319. doi: 10.1038/nbt.3820
        • Ewels, P. A., Peltzer, A., Fillinger, S., Patel, H., Alneberg, J., Wilm, A., Garcia, M. U., Di Tommaso, P., & Nahnsen, S. (2020). The nf-core framework for community-curated bioinformatics pipelines. Nature Biotechnology, 38(3), 276-278. doi: 10.1038/s41587-020-0439-x
        • Grüning, B., Dale, R., Sjödin, A., Chapman, B. A., Rowe, J., Tomkins-Tinch, C. H., Valieris, R., Köster, J., & Bioconda Team. (2018). Bioconda: sustainable and comprehensive software distribution for the life sciences. Nature Methods, 15(7), 475–476. doi: 10.1038/s41592-018-0046-7
        • da Veiga Leprevost, F., Grüning, B. A., Alves Aflitos, S., Röst, H. L., Uszkoreit, J., Barsnes, H., Vaudel, M., Moreno, P., Gatto, L., Weber, J., Bai, M., Jimenez, R. C., Sachsenberg, T., Pfeuffer, J., Vera Alvarez, R., Griss, J., Nesvizhskii, A. I., & Perez-Riverol, Y. (2017). BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics (Oxford, England), 33(16), 2580–2582. doi: 10.1093/bioinformatics/btx192
        Notes:
        • The command above does not include parameters contained in any configs or profiles that may have been used. Ensure the config file is also uploaded with your publication!
        • You should also cite all software used within this run. Check the "Software Versions" of this report to get version information.

        nf-core/rnavar Workflow Summary

        Input/output options

        input
        /work/user/fmt116/TP_nextflow/projet_nextflow/sra_tools/input.csv
        outdir
        /work/user/fmt116/TP_nextflow/projet_nextflow/sra_tools/results_rnavar

        Alignment options

        star_index
        /work/user/fmt116/TP_nextflow/projet_nextflow/sra_tools/star_index/

        Variant filtering

        gatk_vf_fs_filter
        30.0
        gatk_vf_qd_filter
        2.0

        Pipeline stage options

        skip_baserecalibration
        true

        Reference genome options

        fasta
        /work/user/fmt116/TP_nextflow/projet_nextflow/sra_tools/GCF_902167405.1_gadMor3.0_genomic.fna
        gtf
        /work/user/fmt116/TP_nextflow/projet_nextflow/sra_tools/genomic.gtf
        snpeff_db
        GRCh38.105
        vep_cache_version
        115
        vep_genome
        GRCh38
        vep_species
        homo_sapiens

        Generic options

        trace_report_suffix
        2025-10-02_14-34-26

        Core Nextflow options

        configFiles
        /home/fmt116/.nextflow/assets/nf-core/rnavar/nextflow.config
        containerEngine
        singularity
        launchDir
        /work/user/fmt116/TP_nextflow/projet_nextflow/sra_tools
        profile
        singularity
        projectDir
        /home/fmt116/.nextflow/assets/nf-core/rnavar
        revision
        1.2.1
        runName
        jolly_mcclintock
        userName
        fmt116
        workDir
        /work/user/fmt116/TP_nextflow/projet_nextflow/sra_tools/work

        MultiQC v1.30 - Written by Phil Ewels, available on GitHub.

        This report uses Plotly, jQuery, jQuery UI, Bootstrap and FileSaver.js.